ImSpectR
R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data
Martijn Cordes (Leiden University Medical Center)
Karin Pike-Overzet (Leiden University Medical Center)
Marja van Eggermond (Leiden University Medical Center)
Sandra Vloemans (Leiden University Medical Center)
Miranda R. Baert (Leiden University Medical Center)
Laura Garcia-Perez (Leiden University Medical Center)
Frank J.T. Staal (Leiden University Medical Center)
Marcel J.T. Reinders (Leiden University Medical Center, TU Delft - Pattern Recognition and Bioinformatics)
Erik B. van den Akker (Leiden University Medical Center, TU Delft - Pattern Recognition and Bioinformatics)
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Abstract
An effective immune system is characterized by a diverse immune repertoire. There is a strong demand for accurate and quantitative methods to assess the diversity of the immune repertoire for various (pre-)clinical applications, including the diagnosis and prognosis of primary immune deficiencies, or to assess the response to therapy. Current strategies for immune diversity assessment generally comprise the visual inspection of the length distribution of rearranged T- and B-cell receptors. Visual inspections, however, are prone to subjective assessments and thus lead to biases. Here, we introduce ImSpectR, a unified approach to quantify immunodiversity using either spectratype, repertoire sequencing or single cell RNA sequencing data. ImSpectR scores various types of deviations from the expected length distribution and integrates these into one measure, allowing for robust quantitative comparisons of immune diversity across individuals or conditions.
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